Shinegan: The Secret is in the Eyes
by Meara10
Summary: She never had an easy life. Surrounded with mystery, Aira is brought to Konoha where she is accepted with open arms. But things aren't always as it seems. Death, rivalry, love and hate. Her journey begun when she met one blond boy: Uzumaki Naruto. But who is the man with the red eyes that seem to hunt her thoughts? Find out for yourself.
1. Chapter 1: Breaking the cage

Something was happening outside the doors of her cage. She could feel and hear them.

Her eyes were closed, her was body relaxed and her ears were sharpened by the never-ending darkness.

"...Anyone here?" Her small voice carried around the room but only the soft echoes answered her.

A heavy sigh made its way through her as she wiggled around trying to free her hands by twisting and pulling on her restraints. The long steeled chains were tight on her wrists, making it painful to move them.

She squinted to see past the blindfolds over her eyes but she couldn't make out anything through the darkness, making her Kekkei Genkai completely useless.

She suspected that it was her strange abilities that had put her in such a dangerous situation in the first place. She released another sigh but this time it was answered by another sound.

"Footsteps" She whispered. They weren't just any footsteps, they were stealthy and light footsteps belonging to shinobi. That meant that in the next moments she would either be free of meet an early death.

With this thought, she patiently waited.

After a little while, she could hear the sounds of clashing kunai. Screams and groans of agony from her captors that resonated in her ears before all fell quiet. This eerie silence made her fears and anticipation grow as her heart started to beat fasted.

_I have a chance to finally get out of here._

The rush of emotions in her was cut short when the door to her room creaked open. She make out who it was, only a mixture of darkened shapes danced through her blindfolds so she stayed quiet, waiting for the unavoidable outcome.

She could make out a single set of footsteps growing louder as they made its way towards her. They suddenly stopped sharply and she breathed in deeply and stayed still, hoping that the person did not want to harm her. It was quiet for a moment before she heard the scrunching of the person's clothing as he crouched down to her level.

With one swift move from the stranger, her blindfolds were taken off and blinding light assaulted her purple eyes.

Ibiki was leading his team of ANBU through the complicated maze-like tunnels of the enemy base. A report was made a few days ago that enemies had made an underground headquarter near the village and were currently keeping deadly weapons in their mist. His team had been dispatched soon after the information was proven true.

"Captain, we sense enemies ahead." An ANBU member announced.

"Let's split up. Half of us will go back and search for any weapons, scrolls or anything threatening and the other half will go on ahead and kill these low-lives." Ibiki ordered, splitting his team into groups. "We will meet back at the entrance in half an hour."

"Is it wise to split up, Ibiki-sensei? What if they use the strong weapons the Hokage mentioned, won't we need all the backup we have?" A female voice rang out. Her cat-like ANBU mask drawn with swirls of red and orange.

"No, these enemies aren't strong ninja. They are just a group of runt ninja trying to prove something by getting power using violence." He answered roughly to her and they nodded in understanding. They split up and each group went their own way. Ibiki's small group went ahead and easily defeated the enemy. As he had claimed, the shinobi in this organization were weak and not well trained.

"What's that sound?" Some ANBU asked as he heard the rattling of chains.

"It came from there." The same female ANBU from earlier answered, pointing at a strange golden door that was closed shut by locks and chains.

Ibiki's eyes narrowed at the door. "Let's go." He tried to open the locks but they wouldn't budge under his strong grip. "There has to be some kind of sealing jutsu."

"What could be in there that they had to seal the room shut?" She questioned her leader.

"I'm not sure but we will find out soon." He quickly signed and the seals on the door fell to the ground. He grabbed onto the door and pushed it open.

_What the hell?_

He had been expecting a dangerous animal or maybe a dangerous prisoner but a small child, probably no older than twelve sat in the middle of the room chained and blindfolded.

Her black hair was tousled and matted but she seemed unhurt. She had slight bruises on her arms and legs but she sat up straight and her posture was relaxed as if she had known they were coming.

_Odd._

He quickly went to her and took off her blindfolds, her eyes stayed closed for a moment before they slowly opened. The violet hues of them took him by surprised. Never had he seen a color of eyes like her.

She squinted at him for a moment as her eyes readjusted to the light.

"Are you okay?" His gruff voice assaulted her ears, surprising her at his proximity. He quickly looked over her, she was pale but looked healthy.

Her captors had clearly taken good care of her. Ibiki took another look at the girl once again to reevaluated the damages on her body only to find her staring at him.

He had expected to see fear but the emotions in the pale amethyst in her eyes was that of curiosity. "I am fine."

"What is your name, kid?" Ibiki questioned as he undid the restrain of her wrists, they were very bruised.

"My name is Aira. Who are you?" She asked calmly, raising a brow at the nickname he had given her.

"Morino Ibiki, Commanding officer of Torture and Interrogation Force of the Village hidden in the Leaf." His name resonated power and safety to her. She knew that Konoha was a village of peace.

"Konohagakure?" Her eyes glazed over in thought and as she snapped back to reality, she shook her head and chuckled. "I haven't hear that name in a very long time. Why are you here?"

"The real question is why are_ you_ here?" He countered amused at all the questions she was calmly asking. She made no sign that she was in a hurry to escape her prison. If it had been him in her shoes, he would have wanted to get out as fast as possible.

"I was kidnapped a few years back." She told him. "They have kept me here waiting for someone to buy me."

Ibiki wondered what a group or criminals would want with a small little girl, apart from the obvious lustful actions that certain criminals liked to inflict on children. It didn't seem like they had touched her. At least, if they did she was not showing signs of it.

It led him to the curious thought that maybe she was one of the weapons, although very doubtful or maybe that she was a princess or a feudal Lord's daughter held captive for some heavy ransom.

"Hey-" Her soft and mature voice snapped me out of my thoughts. "- can you get me out of here?"

He nodded and offered his hand to help her up.

"Let's go back to Konoha" He led her outside the room.

"I guess there is no avoiding it now." Aira muttered to herself, out of option. "Lead the way, chief of interrogation." She mocked him with a grin.

He stared down at her with seriousness as silence settled between them. He didn't liked to be teased but none-the-less urged his team forward, holding back a smirk when Aira pouted at his lack of reaction.

_She is something._


	2. Chapter 2 : Starting Anew

Sunlight.

_It's been to long._

"It will take time for them to adjust." Aira heard Ibiki announce in her direction. She stared at him in question. "Your eyes. They'll take time to adjust to the light." He rephrased to her, looking slightly amused.

She nodded in understanding and followed after him, as he ran forward and away from the burning hideout.

"Hey kid. Can I ask you something?" She frowned at the childish endearment but noticed the amusement in his eyes. She reluctantly agreed to his question as their group started jumping from tree to tree.

She struggled to follow, her breath coming out in short pants.

"Before you were kidnap, where did you live?" Ibiki asked.

"Do you mean which village?" He gave her a nod as a response.

"I don't remember. I was young when they took me." She swiftly lied between short intakes of breath, her lungs burning at the hard physical exercise.

If Ibiki didn't believe her lie, he hadn't said anything. He picked her up as she was slowing down and carried her the rest of the way.

Pretty soon, they could see the gates of Konoha in the distance: two big green doors with a yellow roof to match it off.

The sign of the village hidden in the leaf was emblemed on top of the gates.

This was all too familiar for her.

While they made their way through the gates, two ninjas who were keeping guard of the gate stopped them.

"Who's this Ibiki?" One of the guards asked. He had dark pointy hair with some bandage on his nose, the leaf headband proudly shown on his forehead.

"Is this a hostage?" The other one asked. This one also had dark hair but one eye was hidden beneath it, the leaf headband covering most of his hair.

"This is Aria. She was a hostage of the Orimi organization." Ibiki told them.

Aira could see a slight frown marring their faces at the news, she gave them a small smile as if to ease their worry.

"I'm Hagane Kotetsu and this is Kamizuki Izumo" The first guard returned her smile.

"We should get going. I have to report to the Hokage." Ibiki interrupted their introduction.

Aira frowned. "That was rude." Ibiki ignored her and led her to the Hokage's building.

They arrived at a large building with the symbol for fire embedded in a red circle. Aira noted the faces of all the past Hokage engraved on the cliff behind the building.

They entered and ventured up to a door on the last floor, which she suspected was the current Hokage's office. Ibiki knocked on the door, they heard a small 'come in' and, as instructed, went in.

A rather old man greeted them behind his large wooden desk, he was smoking a pipe and looking through his paper work.

He smiled. "Well what do we have here?"

"My name is Otsukijou Aira" She answered politely.

Recognition filled his features as he registered her name.

_Does he know me?_

"I came to give my report on the mission, sir Hokage. The mission was successful and we secured the weapons."Ibiki's voice snapped them both to attention. "I found her held hostage as well."

The Hokage nodded , a deep thought marring his face. "I understand. Have we contacted her family and village?"

Ibiki looked down at Aira, urging her to answer his question. "I would like to stay here if possible."

The Hokage didn't question her further. "Very well. If you wish to stay you may as well attend the ninja academy. Being a shinobi is a good way to make a living if you have no family business to take over."

"I'd like that very much. I trained a little bit back in my home village." She agreed, instantly liking the idea of school.

He chuckled at her. "Perfect! You may go to the academy now and your teacher will be informed of your arrival. I need to talk to Ibiki alone." He finished.

Aira bowed her head and left, feeling dismissed. Obviously, they had more to talk about.

She wondered the streets, glancing around unsure of her new found freedom. People smiled at her and greeted her into their shops and very soon she felt at home.

"Watch out!"

She heard the warning yell before she say the orange flash that knocked her to the ground. She quickly got up and glanced around confused.

A group of leaf shinobi ran past her, knocking her down again.

She got up and this time went after them. She could see a blond haired boy running away from the group and instantly wondered what he had done. She saw him jump down and hid behind a bush as they passed him.

She stopped running.

"You can come out now. They're gone." Aira whispered behind him.

He jumped up in surprised and tripped over the bush.

Aira observed him in curiosity as he sheepishly smiled.

_What a nice smile._

"You scared me!" He rose from the ground. "I haven't seen you around before. I'm Uzumaki Naruto, future Hokage. Believe it!" He held out his hand for her to shake.

Slight worry rose in his gut as she slightly hesitated at the touch but his smile didn't falter. She noticed and quickly grabbed his hand as he was starting to retreat it.

"My name is Aira." She smiled at him, happy to have met someone new. "Do you think you could help me find the aca-"

"Naruto!"

Their conversation was interrupted as a man appeared behind Naruto and grabbed onto his ears. The man's hair was tied in a ponytail and he had a scar running across his nose. He appeared young enough to her.

He started to scream at him as Naruto tried to make excuses. Aira observed them, silently.

After a while, the man that Naruto called Iruka-sensei, finally took notice of the young girl watching them. "I haven't seen you before. Are you possible Aira-chan?"

She nodded, puzzled.

"You must be my new student then. I'm Umino Iruka but all my students call me Iruka-sensei so feel free to do so." He told her with a smile before grabbed onto Naruto and led them to the academy.

It wasn't long before she was standing in front of a classroom full of children her age.

_I'm a bit nervous now._

"Well class since Naruto, here, missed the lesson! We will _all_ be practicing the transformation justu!" He yelled to the class, but it was more directed to Naruto.

Groans and whines exploded in the classroom.

He turned around. "Also we have a new student that will be joining us." Everybody's attention went straight to Aira. "Her name is Aira. Please make her feel welcome."

The students then started to form a line in front of the class. She joined in doing the exercise, hoping to participate in the class.

She made her way towards the line and went behind Naruto. The first to take their turn was a girl with pink hair.

"Transformation Jutsu!" she yelled and transformed into Iruka. Iruka praised her and called for the next person but not before the pink head called "Did you see that Sasuke-kun?"

The boy, Sasuke, ignored her and she pouted in disappointment before it was his turn to go upfront.

"Okay. Uchiha Sasuke." Iruka called.

_Uchiha?_

His name sparked recognition in Aira and she winced at the sharp pain that exploded in her head.

"Tranform." Sasuke muttered before transforming as well, receiving a praised to which received a short grunt from Sasuke.

Next, Iruka called for Naruto. Naruto made his way towards the front and called out 'transform' but instead of transforming into Iruka, he became a naked and female version of himself.

Aira cracked a laugh as Iruka started to scream some more at Naruto. It might have been a prank but she had to admit that the proportions and the colors of the transformation were good.

"Otsukijou Aira." Iruka called next, not expecting her to be able to perform the transformation as well as her peers but she went up and quickly performed the jutsu without much trouble. "Very good, Aira-chan!"

The class ended soon after and Iruka announced that tomorrow would be the genin exam. Iruka pulled Aira to the side of the class and told her that it was to her discretion whether she wanted to take the exam or wait until the year after.

He then walked her to her new apartment. A small one bedroom house that the Hokage had prepared for her.

"Since no other apartments were left, the Hokage had no choice but to put you in a jonin apartment building. I hope that's fine with you?" Iruka apologized.

She thanked him and he left after he made sure she was comfortable in her new home. She fell asleep soon after, her thoughts going back to the name '_Uchiha'_.


	3. Chapter 3: Genin Exam

Aira groaned as she heard her alarm clock ringing in her ears.

She hopped off of her single bed and quickly took a shower. She got out and grabbed a soft blue towel, drying her long black hair with it. She noticed on the the side of her sink a pile of clothing with a small black card laying on top.

_For a new beginning - the Hokage._ She read.

She grabbed her new set of clothing and got dressed. The tight navy top with long sleeves fit perfectly. Over it, she wore a shorter and looser sandy brown colored shirt. The collar was high and the sleeves were long as well. She tied a silver buckle vest just below the chest and slipped on the plain black shorts.

_That man had a sense of style._

She took a glance in her mirror and brushed her long hair away from her face, she ran a finger over her right eye softly before changing her mind and brushing it back over it.

She put on her sandal and opened her front door to reveal a grinning Naruto.

"How did you know I lived here?" She asked a bit scared of the answer.

He grinned "I asked Iruka-Sensei. Today is the Genin exam. I am finally getting one step closer to becoming Hokage but first ramen!"

He grabbed her and dragged her to this little restaurant. The owner who went by the name of Teuchi, took their order.

"I've never eaten ramen before." Aira mentioned to them.

"What?!" Naruto exclaimed.

"Also I didn't bring my wallet." She awkwardly laughed.

He grinned. "No problem! I'll feed you."

After Naruto finished his eleventh bowl of ramen, they finally headed off for the academy.

They entered their classroom and walked over to his seat. Aira took the free seat between him and the Uchiha boy.

Sasuke glanced at her from the corner of his eye as he felt the bench shift. He through an annoyed expression to her way before turning his head in the other direction, resting his head in his palm.

Aira felt a wave of nostalgia but she shrugged the thought away and began talking to Naruto until a commotion in the door way of the class distracted them from their conversation.

"I arrived first, Ino-pig!" The pink haired girl screamed as she passed the classroom doors.

"No way, I was here first billboard brow!" A blond girl, Aira assumed her name was Ino, screamed as she reached the classroom at the same time.

"No way, I was here first so I get to sit next to Sasuke-kun" Sakura replied confidently.

_So this is what this is about._

"Pathetic." Sasuke muttered as he heard his name cross her lips but Aira had heard.

"And you're rude." She whispered back to him.

He turned around to look at her but didn't say anything. He scowled at her before turning away once more.

He was a typical Uchiha. They were all mysterious and gorgeous, it seemed it was in their genes to attract the female population. They were dangerous to all the hearts out there.

Well that's what Naruto had told her yesterday.

Aira turned around to resume their conversation just to discover that Naruto was gone. She glanced around the room but found him crouching in front of Sasuke. His feet were firmly planted on their desk as he and Sasuke stared daringly into each others eyes but when the guy sitting in front, leaned back onto his seat, he bumped Naruto forward.

He fell into Sasuke, lips against lips.

Aira started to laugh loudly while both Sasuke and Naruto started to spit on the ground and try to wash their mouths with the back of their sleeves.

After some death threats and a beat up Naruto, courtesy of Sasuke's lovers, Iruka finally arrived.

"Class, we are gonna start the genin exam. You will be performing the clone jutsu." Aira could feel the panic rising inside Naruto so she gave him a reassuring smile. "Now, we'll start with Aira."

She followed their sensei into another classroom. Iruka sat beside another male shinobi with white hair who gave her a faux smile.

"Please create three clones" He instructed her.

Aira made the hand signs and successfully made the clones. This was something she had learned to performed as a younger child.

After passing with flying colors, she retired home, fully expecting to see Naruto among the graduates the next day.

She spend the rest of her say studying some Konoha politics before slipping into a deep sleep.

It was hours before she was woken up by a commotion outside her door.

She made her way out of the bedroom and past the living room, slightly tripping on the white carpet at her feet before putting her ear on the door.

"He stole it! Naruto stole the forbidden scroll."

_What?_

She ran back to her room, tripping on her carpet again before throwing on her clothing. She jumped through her window and jumped from rooftop to rooftop.

"He must be here somewhere." She muttered as she surveyed the village. She saw a flash of white and orange through some tree lines and followed after it.

She approached carefully, not wanting to give herself away. She saw the silhouette of three people. The first was Naruto.

"You're the nine-tailed fox, Naruto!" She heard a familiar voice scream.

Aira approached a little more and saw Iruka and the other sensei who had been at the examination.

Naruto performed a series of hand signs. "Kage Bunshin no Jutsu."

Hundreds of Naruto clones appeared through the smoke. His clones began to attack the white haired shinobi who couldn't do much but let himself get beat up.

Aira was confused to say the least. She had cleared missed an important part but Iruka seemed to support Naruto.

_Did they say that Naruto was a... jinchuuriki?_

She quietly observed him and he tended to Iruka who was injured.

To be truthful, Naruto didn't seem like much to Aira but now she believed there was more to him that met the eyes. She them for a little lonegr as Iruka and Naruto exchanged a few words. Iruka handed Naruto his headband, congratulating him for passing his exam.

_Naruto didn't pass the genin exam?_

Naruto started to cry. His nose and eyes started to water as he engulfed Iruka in a big hug. Aira quietly chuckled as Iruka tried to pry Naruto off him before leaving them to their moment.

_I hope Naruto and I end up on the same team._


End file.
